Contacts of the helix formed by residues 72 - 81 (chain A) in PDB entry 6MOL
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A HIS* 3.6 5.0 - - - -
63A VAL 5.1 1.8 - - - -
64A ASN* 4.9 7.6 - - + +
65A ALA 3.3 13.9 - - - +
66A SER* 4.9 4.5 - - - -
70A GLY 4.0 9.9 - - - +
71A THR* 1.3 80.1 - - - +
73A PRO* 1.3 74.1 - - - +
74A LEU* 3.8 7.0 + - - +
75A HIS* 2.9 41.6 + - + +
76A LEU* 3.2 10.0 + - - +
95A ASP* 6.2 0.7 - - + -
98A ALA* 4.1 22.5 - - + +
99A TYR 5.4 1.8 - - - +
106A PRO* 5.3 0.7 - - - +
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Residues in contact with PRO 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LEU* 4.0 36.3 - - + +
42A HIS* 3.2 28.7 - - + +
45A ALA* 3.8 9.7 - - + +
62A ASP 4.1 5.2 - - - +
63A VAL 3.4 26.2 - - - +
65A ALA* 3.4 8.5 - - + +
72A THR* 1.3 87.8 - - - +
74A LEU* 1.3 60.2 + - - +
76A LEU* 3.4 3.2 + - + +
77A ALA* 3.2 17.7 + - - +
89A LEU* 3.5 18.1 - - + +
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Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A VAL 4.9 1.9 + - - +
72A THR* 3.2 7.0 + - - +
73A PRO* 1.3 76.7 - - - +
75A HIS* 1.3 65.3 + - - +
77A ALA 3.5 0.5 + - - -
78A ALA* 3.0 24.1 + - + +
86A VAL* 4.2 18.2 - - + +
89A LEU* 3.8 29.0 - - + +
90A LEU* 3.7 33.4 - - + -
94A ALA* 4.1 11.9 - - + -
95A ASP 3.4 27.6 - - - +
96A VAL* 4.0 3.6 - - - -
106A PRO* 3.8 23.1 - - + -
122A LEU* 4.2 4.3 - - + -
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Residues in contact with HIS 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A THR* 3.7 18.6 - - + -
72A THR* 2.9 35.0 + - + +
74A LEU* 1.3 78.6 - - - +
76A LEU* 1.3 57.3 + - - +
78A ALA* 3.3 3.8 + - - +
79A THR* 2.8 34.8 + - - -
98A ALA* 3.3 20.4 + - + -
99A TYR* 4.0 7.2 - - - -
100A ASP* 4.0 10.8 - - + +
104A ALA 2.7 25.5 + - - -
105A THR 3.6 3.1 - - - -
106A PRO* 3.3 36.4 - - + +
109A LEU* 3.7 19.6 - - + +
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Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A HIS* 3.4 51.1 - - + +
45A ALA* 4.6 2.0 - - + -
46A LEU* 3.8 39.0 - - + +
71A THR* 3.9 21.3 - - + -
72A THR 3.2 2.9 + - - +
73A PRO 3.8 5.8 - - - +
74A LEU 3.3 0.2 - - - -
75A HIS* 1.3 79.2 - - - +
77A ALA* 1.3 62.3 + - - +
79A THR* 3.3 4.5 + - - +
80A MET* 3.0 35.3 + - + +
110C HIS* 4.3 22.9 - - + +
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Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ALA* 4.2 11.1 + - + +
73A PRO 3.2 14.3 + - - +
74A LEU 4.0 2.5 - - - +
75A HIS 3.3 0.2 - - - -
76A LEU* 1.3 78.5 - - - +
78A ALA* 1.3 57.3 + - - +
81A GLY* 3.1 21.7 + - - -
82A HIS* 3.2 14.3 + - + +
85A ILE* 3.8 28.3 - - + -
86A VAL* 3.6 21.6 - - + +
89A LEU* 3.9 7.2 - - + -
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Residues in contact with ALA 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A LEU* 3.0 19.5 + - + +
75A HIS* 3.8 3.6 - - - +
77A ALA* 1.3 76.2 - - - +
79A THR* 1.3 64.5 + - - +
81A GLY* 3.9 0.5 + - - -
86A VAL* 4.1 3.1 - - + +
106A PRO* 3.6 34.3 - - + +
109A LEU* 4.9 1.3 - - + -
110A ALA* 3.8 15.2 - - + +
115A HIS* 3.6 17.3 - - - -
118A ILE* 4.3 20.8 - - + +
122A LEU* 4.6 1.3 - - + -
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Residues in contact with THR 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A HIS 2.8 21.3 + - - -
76A LEU* 3.3 7.7 + - - +
78A ALA* 1.3 75.6 - - - +
80A MET* 1.3 82.5 + - + +
109A LEU* 3.2 28.5 - - + +
113A MET* 3.3 47.7 - - + +
115A HIS* 3.5 3.8 + - - -
109C TYR* 6.3 1.8 - - + -
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Residues in contact with MET 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LEU* 3.8 31.4 - - + +
76A LEU* 3.0 18.6 + - + +
79A THR* 1.3 101.2 - - + +
81A GLY* 1.3 60.6 + - - +
82A HIS* 3.4 26.8 - - + +
115A HIS* 3.2 14.1 + - - -
25C GLU* 5.8 2.9 - - - +
110C HIS 3.3 28.0 - - - +
111C ARG* 4.0 20.4 - - + -
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Residues in contact with GLY 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ALA 3.1 9.7 + - - -
78A ALA 3.9 1.3 + - - -
79A THR 3.4 1.8 - - - -
80A MET* 1.3 79.2 - - - +
82A HIS* 1.3 64.9 + - - +
83A LEU* 3.6 4.9 + - - +
115A HIS* 3.5 29.7 + - - -
118A ILE* 4.0 10.9 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il